Double stranded linear nucleic acid probe

ABSTRACT

A double-stranded nucleic acid hybridization probe and methods of using the same are described. The probe described is particularly suited for real-time RT-PCR reactions and has high tolerance to mismatches.

This application claims priority to the provisional application Ser. No.60/526,480 filed on Dec. 3, 2003.

FIELD OF INVENTION

The invention relates generally to the field of nucleic acidamplification and detection. Additionally, the invention relates tocompositions and methods for performing PCR and probe hybridizationusing a single reagent mixture.

BACKGROUND

DNA-based analyses are used routinely in a wide spectrum of settings,including clinical hematology, molecular genetics, microbiology andimmunology. Many current techniques rely on PCR amplification of apolynucleotide of interest (hereinafter “target molecule”) inconjunction with several types of post-amplification detectiontechniques. Other non-PCR based amplification techniques are well knownin the art including, but not limited to, oligo ligation assay (OLA),ligase chain reaction (LCR), transcription-mediated amplification (TMA),and strand displacement amplification (SDA). Additionally, thesetechniques are amenable to mixing. That is, the product of oneamplification reaction can be used as the target of anotheramplification reaction, which allows great sensitivity with anadditional step that tends to increase sensitivity.

One preferred amplification format is known as a real-time homogeneousassay. A real-time assay is one that produces data indicative of thepresence or quantity of a target molecule during the amplificationprocess, as opposed to the end of the amplification process. Ahomogeneous assay is one in which the amplification and detectionreagents are mixed together and simultaneously contacted with a sample,which may contain a target nucleic acid molecule. Thus, the ability todetect and quantify DNA targets in real-time homogeneous systems asamplification proceeds is centered in single-tube assays in which theprocesses required for target molecule amplification and detection takeplace in a single “close-tube” reaction format. For example, currenttechniques that use PCR amplification and have these features aregenerally known as Real-Time PCR techniques. Similarly, non-PCR-basedtechnologies are also within the skill of the ordinary artisan and areamenable to homogeneous detection methods.

In most amplification and detection techniques a probe is used to detectan amplification product. Several probe systems known in the art utilizea fluorophore and quencher. For example, molecular beacon probes aresingle-stranded oligonucleic acid probes that can form a hairpinstructure in which a fluorophore and a quencher are usually placed onthe opposite ends of the oligonucleotide. At either end of the probeshort complementary sequences allow for the formation of anintramolecular stem, which enables the fluorophore and the quencher tocome into close proximity. The loop portion of the molecular beacon iscomplementary to a target nucleic acid of interest. Binding of thisprobe to its target nucleic acid of interest forms a hybrid that forcesthe stem apart. This causes a conformation change that moves thefluorophore and the quencher away from each other and leads to a moreintense fluorescent signal. Molecular beacon probes are, however, highlysensitive to small sequence variation in the probe target (Tyagi S. andKramer F. R., Nature Biotechnology, Vol. 14, pages 303-308 (1996); Tyagiet al., Nature Biotechnology, Vol. 16, pages 49-53(1998); Piatek et al.,Nature Biotechnology, Vol. 16 pages 359-363 (1998); Marras S. et al.,Genetic Analysis: Biomolecular Engineering, Vol. 14, pages 151-156(1999); Tapp I. et al, BioTechniques, Vol 28, pages 732-738 (2000)).

Unlike molecular beacon probes, some single-stranded linear probespossessing also a quencher and a fluorophore attached at opposite endsof an oligonucleotide do not form a hairpin structure. Instead, thiskind of linear oligonucleotide probes in solution behaves like a randomcoil, its two ends occasionally come close to one another, resulting ina measurable change in energy transfer. However, when the probe binds toits target, the probe-target hybrid forces the two ends of the probeapart, disrupting the interaction between the two terminal moieties, andthus restoring the fluorescent signal from the fluorophore. In addition,single-stranded linear probes can be designed as “TaqMan probes”, thatbind to target strands during PCR and thus can be enzymatically cleavedby the 3′ exonuclease activity of the Taq DNA polymerase during theprimer extension phase of the PCR cycle resulting in an increase influorescence in each cycle proportional to the amount of specificproduct generated. It has been reported that long single-stranded linearprobes suffer from high “background” signals, while shorter ones aresensitive to single-base mismatches (Lee L. G. et al., Nucleic AcidsResearch, Vol. 21, pages 3761-3766 (1993); Täpp I. et al. (above); U.S.Pat. No. 6,258,569; U.S. Pat. No. 6,030,787).

Double-stranded linear probes are also known in the art. Double-strandedlinear probes have two complementary oligonucleotides. The probesdescribed in the prior art have been of equal length, in which at leastone of the oligonucleotides acts as a probe for a target sequence in asingle-stranded conformation. The 5′ end of one of the oligonucleotidesis labeled with a fluorophore and the 3′ end of the otheroligonucleotide is labeled with a quencher, e.g., an acceptorfluorophore, or vice versa. When these two oligonucleotides are annealedto each other, the two labels are close to one another, therebyquenching fluorescence. Target nucleic acids, however, compete forbinding to the probe, resulting in a less than proportional increase ofprobe fluorescence with increasing target nucleic acid concentration(Morrison L. et al., Anal. Biochem., Vol. 183, pages 231-244 (1989);U.S. Pat. No. 5,928,862).

Double-stranded linear probes modified by shortening one of the twocomplementary oligonucleotides by few bases to make a partiallydouble-stranded linear probe, are also known in the art. In suchdouble-stranded linear probes in the prior art, the longeroligonucleotide has been end-labeled with a fluorophore and the slightlyshorter oligonucleotide has been end-labeled with a quencher. In thedouble-stranded form, the probe is less fluorescent due to the closeproximity of the fluorophore and the quencher. In the presence of atarget, however, the shorter quencher oligonucleotide is displaced bythe target. As a result, the longer oligonucleotide (in the form ofprobe-target hybrid) becomes substantially more fluorescent.

The double-stranded probes known in the prior art havingoligonucleotides of unequal lengths display complete discriminationbetween a perfectly matched target and single nucleotide mismatchtargets. Also, these probes do not have optimal reaction kineticsespecially when low quantities of target nucleic acid are present. (Liet al., Nucleic Acids Research, Vol. 30, No. 2, e5 (2002))

The detection of viral RNAs presents certain challenges, which are notpresented by the desire to detect DNAs of interest. The probes of theprior art are suitable for the detection of viral RNAs, but could beimproved. First, some viral RNA targets are prone to rapid mutation inthe bodies of their hosts. To ensure that mutated viral RNA sequencesare detected along with so-called “wild-type” sequences, nucleic acidprobes used to detect viral RNAs should be tolerant of mismatches, yetstill specific enough to avoid interaction with non-target nucleicacids. (i.e., false-positive results). Many of the probes of the priorart are sensitive to single-nucleotide changes, and therefore, are notoptimal for the detection of viral nucleic acids.

Additionally, viral RNAs often must be reverse transcribed into DNAbefore amplification of a nucleic acid sequence of interest.Unfortunately, it has been discovered by the present inventors that someprior art nucleic acid probes can interfere with the reversetranscription (i.e., enzymatic copying of RNA sequences into DNAsequences).

It is also desirable that nucleic acid probes be capable of sensitivelydetecting both small and large quantities of nucleic acids of interest.Some nucleic acids probes of the prior art are not well suited todetecting small quantity of nucleic acids of interest. Other nucleicacids probes of the prior art are not well suited to the sensitivedetection of large quantities of nucleic acids.

In view of the above, there is a need for a probe in which: a) thesequences can be readily manipulated, b) the oligonucleotides are easyto design without the limitation of being capable of forming stem orloop, c) there is high tolerance to mismatches, and/or d) theoligonucleotides are suitable for real-time RT-PCR reactions.

SUMMARY OF THE INVENTION

The present invention relates generally to double-stranded nucleic acidhybridization probes and methods of using the same. The probe of thepresent application can be used in any suitable manner, and isparticularly well suited for PCR amplification and probe hybridizationusing a single reaction vessel and a single reagent mixture.

The present invention provides a nucleic acid probe that comprises afirst oligonucleic acid and a second oligonucleic acid. The firstoligonucleic acid is labeled by a fluorophore and is substantiallycomplementary to a nucleic acid of interest, such that when the nucleicacid of interest is present, the first oligonucleic acid can bind to thenucleic acid of interest. The second oligonucleic acid has a quenchermolecule and is substantially complementary to the first oligonucleicacid. Accordingly, the first and second oligonucleic acids can bindtogether to form a double-stranded nucleic acid. When the firstoligonucleic acid is bound to the second oligonucleic acid, thefluorescent emission of the fluorophore attached to the firstoligonucleic acid is quenched (i.e., detectably less than the emissionof the same fluorophore when the first oligonucleic acid and secondoligonucleic acid are not bound together). Binding of the firstoligonucleic acid to the nucleic acid of interest, therefore, increasesthe fluorescence in a test system, thereby indicating whether thenucleic acid of interest is S present. The first oligonucleic acidcomprises “m” contiguous nucleobases substantially complementary to anucleic acid of interest, and the second oligonucleic acid comprises “n”contiguous nucleobases substantially complementary to the firstoligonucleic acid, wherein “m” and “n” are independently selectedintegers, and when m is less than 25, n is up to one half of m; when mis 26 to 29, n is from 8 to 13; when m is 30 to 34, n is from 8 to 15;when m is 35 to 39, n is from 8 to 20; when m is 40 to 44, n is 9 to 25;when m is 45 to 49, n is 10 to 30; when m is 50 to 54, n is 10 to 35;when m is 55 to 59, n is 10 to 40; when m is 60 to 64, n is 11 to 45;when m is 65 to 69, n is from 11 to 50; when m is 70 to 75, n is from 15to 55.

The present invention also provides a nucleic acid probe in which thefirst and longer oligonucleic acid is substantially complementary to anucleic acid of interest and comprises a quencher. The second, andshorter, oligonucleic acid comprises a fluorophore. The firstoligonucleic acid is substantially complementary to the secondoligonucleic acid, which permits simultaneous hybridization of the firstoligonucleic acid with the second oligonucleic acid, and quenching ofthe fluorescence of the second oligonucleic acid. When the firstoligonucleic acid is bound to a nucleic acid of interest, the secondoligonucleic acid is displaced and the fluorescent emission of thefluorophore is detectably greater than when it is annealed to the firstoligonucleic acid.

The present invention also provides a method of detecting or quantifyinga nucleic acid of interest in a test sample using any embodiment of thenucleic acid probe of the present invention described herein. Forexample, the present invention provides a method of quantifying RNA in atest sample in which the sample is contacted with nucleic acidamplification reagents and reverse transcription reagents underconditions permissive of reverse transcription, and then/also of nucleicacid amplification such that cDNA is produced and amplified. The mixtureis subsequently or simultaneously contacted with a nucleic acid probe ofthe present invention as described herein, wherein the first and secondoligonucleic acids of the probe do not bind together and/or to thetarget RNA, at the temperature of the reverse transcription step.

The present invention also provides a method of detecting and/orquantifying a nucleic acid of interest in a test sample in which thesample is contacted with DNA amplification reagents to amplify a portionof the nucleic acid of interest, and a first oligonucleic acid probethat has a fluorophore and a quencher, and is specific for the amplifiednucleic acid. Before, during or after the addition of the firstsingle-stranded oligonucleic acid, a second oligonucleic acid comprisinga quencher is added in a ratio so that the second to the firstoligonucleic acids in the mixture can be less than one, and so that thefirst and second oligonucleic acids form a duplex in solution.

DESCRIPTION OF THE DRAWINGS

FIG. 1A-F graphically presents melting curve data of nucleic acid probesof the present invention without or with mismatched targetoligonucleotides (as denoted next to each curve). (A) 520-20/que-16; (B)520-20/que-14; (C) 520-20/que-12; (D) 520-31/que-14; (E) 520-20/que-12;(F) 520-31/que-14. “m” indicates the length of the contiguousnucleobases of the FAM-labeled oligonucleic acid substantiallycomplementary to the target, whereas “n” represents the length of thecontiguous nucleobases of the DABCYL-labeled quenching oligonucleic acidsubstantially complementary to the FAM-labeled oligonucleic acid.

FIG. 2A-C illustrates the comparison of real-time RT-PCR amplificationplots of wild type transcript with those of mutated transcripts (asindicated next to each curve).

FIG. 3A-B graphically presents real-time measurement of ampliconsynthesis during RT-PCR reactions using the partially double-strandedlinear probe set lin-41/que-23 using (A) HIV wild type templatetranscripts and (B) internal control transcript at 100 copies perreaction mixture.

FIG. 4A-B depicts real-time measurements of amplicon synthesis duringRT-PCR reactions using the probe set lin-41/que-22 with (A) HIV wildtype template transcripts and (B) internal control transcript at 100copies per reaction mixture.

FIG. 5A-D graphically presents real-time RT-PCR amplification plot dataof wild type transcript detected by the 1×FAM probe (slin-47), the 2×FAMprobe (dfam-50) or the 3×FAM probe (fain-650) (as indicated next to eachcurve) at the transcript copy number of 10 copies (A), 10e3 copies (B),10e5 copies (C) or 10e6 copies (D) per PCR reaction. Each of the threePAM-labeled linear oligonucleic acid probes was quenched by oligossque-15BH and bhq-5015.

FIG. 6 graphically presents real-time RT-PCR amplification plot data oftranscripts with 0, 2, 3, 4 or 5 mutations (as indicated next to eachcurve).

DETAILED DESCRIPTION

The present invention provides nucleic acid probes as described belowuseful to detect the presence of a nucleic acid of interest (alsocommonly called a target). Of course, the first oligonucleic acid canalso bind to amplified portions of the nucleic acid of interest. Forease of description and understanding, references to nucleic acids ofinterest or “targets” refer both to these moieties as found in a testsample and to amplified copies of portions of these nucleic acids,unless specifically noted to the contrary.

The present invention provides a nucleic acid probe that comprises afirst oligonucleic acid and a second oligonucleic acid. The firstoligonucleic acid is labeled by a fluorophore and is substantiallycomplementary to a nucleic acid of interest, such that when the nucleicacid of interest is present, the first oligonucleic acid can bind to thenucleic acid of interest. For purposes of the present invention, theterm “substantially complementary” means that equal or more than 80% ofnucleobases on one strand of the probe finds its Watson-Crick bindingpartner on the other strand of the probe (or in the nucleic acid ofinterest) in an alignment such that the corresponding nucleotides canhybridize to each other. Binding of the first oligonucleic acid to thenucleic acid of interest prevents the second oligonucleic acid frombinding to the first oligonucleic acid of the probe. The secondoligonucleic acid has a quencher molecule and is also substantiallycomplementary to the first oligonucleic acid. Accordingly, the first andsecond oligonucleic acids can bind together when the nucleic acid ofinterest is not present to form a double-stranded nucleic acid. When thefirst oligonucleic acid is bound with the second oligonucleic acid, thefluorescent emission of the fluorophore attached to the firstoligonucleic acid is quenched (i.e., detectably changed, and preferablylessened, compared to the emission of the same fluorophore when thefirst oligonucleic acid and second oligonucleic acid are not boundtogether). Binding of the first oligonucleic acid to the nucleic acid ofinterest, therefore, changes and preferably increases the fluorescencein a test system, thereby indicating whether the nucleic acid ofinterest is present. In one embodiment, the first oligonucleic acidcontains 15-75 nucleobases (“m”) substantially complementary to target,and the second oligonucleic acid contains “n” nucleobases substantiallycomplementary to the first oligonucleic acid, whereas “n” issignificantly shorter than “m”. The second oligonucleic acid can be ofany suitable length with the primary consideration being that when thenucleic acid of interest is not present, the second oligonucleic acidmust bind with the first oligonucleic acid under temperature and solventconditions in which the probe will be used to infer the presence orabsence of the nucleic acid of interest in a test sample.

Table 1 sets forth preferred and more preferred lengths of the first andsecond oligonucleic acids incorporated into two-stranded probes of thisembodiment of the present invention

TABLE 1 Second Oligonucleic Acid** First Oligonucleic Acid* PreferredMore Preferred <25 <13  6-10 25-30  8-13  8-10 31-34  8-15 10-14 35-39 8-20 12-18 40-44  9-25 12-22 45-49 10-30 15-28 50-54 10-35 25-32 55-5910-40 28-35 60-64 11-45 30-40 65-69 11-50 35-45 70-75 15-55 48-50*Length in nucleobases (“m”) substantially complementary to target.**Length in nucleobases (“n”) substantially complementary to firstoligonucleic acid.

While not desiring to be bound by any particular theory, it is believedthat the long single strand portion of the first oligonucleic acidstrongly favors binding of the first oligonucleic acid to the targetnucleic acid of interest thereby increasing the sensitivity of the probeand under some conditions improving the kinetics of the detectionreaction. Additionally, the longer length of the first oligonucleic acidallows the use of hybridization conditions that permit mismatchhybridization.

Oligonucleic acids are oligomers of naturally occurring or modifiednucleobases. While guanine, adenine, thymine, uridine, cytosine, andoptionally inosine and/or indole, are among the preferred nucleobasesincorporated in the oligonucleic acids of the present invention, anysuitable nucleobase can be incorporated into the probes of the presentinvention. Oligonucleic acids are not necessarily acids or residues ofacids. Rather an oligonucleic acid as used herein is a polymer ofnucleobases or nucleobase analogs that are capable of specificallybinding to a target polynucleotide by way of a regular pattern ofmonomer-to-monomer interactions, such as Watson-Crick type of basepairing, or the like. Most commonly, the monomers are linked byphosphodiester bonds. Less commonly, the monomers are linked by analogsof phosphodiester bonds, such as (deoxyribosyl)phosphonyl polymers orphosphothiorate polymers. Also less commonly employed are peptidenucleic acids, commonly referred to in the art as PNAs, in which thenucleobases are linked in sequence by a polymer containing amide bondsat regular intervals (Nielsen et al., Science, Vol. 254: 1497-1500(1991)).

Methods of synthesizing oligonucleic acids incorporated into probes ofthe present invention are well known in the art and any suitable methodof obtaining the oligonucleic acids of the present invention can beused.

A fluorophore, or a “fluorescent label”, can be any suitable moietycapable of emitting light. The light can be generated chemically,biologically, in response to excitational photons, or from any othersuitable cause. Preferably, fluorophores are fluorescent organic dyesderivatized for attachment to the oligonucleic acids of the probe via alinking moiety. When ribosyl or deoxyribosyl polymers are used to linkthe nucleobases together the dyes can advantageously be derivatized tolink to the terminal 3′ carbon or terminal 5′ carbon of the polymer.

Fluorophores suitable in the context of the present invention include(without limitation) the Violet/Blue dyes (Em_(max) 375-491 nm)7-methoxycoumarin-3-carboxy, AMCA-X (7-aminocoumarin-X), 6-MI or 6-MAP(6-methyl-8-(2-deoy-β-D-ribofuranosyl)isoxanthopteridine); theGreen/Yellow dyes (Em_(max) 492-585 nm) DTAF(4,6-dichlorotriazinyl)aminofluorescein, 6-FAM (fluorescein,6-carboxyfluorescein), Dansyl-X(6-((5-dimethtylaminonaphtalene-1-sulfonyDamino)hexanoate, 6-JOE(6-carboxy-4′,5′-dichloro-2′,7′-dimethoxyfluorescein), HEX(hexachlorofluorescein), BODIPY-TMR-X (tetramethylrhodamine substitute),PyMPO (1-(3-carboxybenzyl)-4-(5-(4-methoxyphenyl)oxazol-2-yl)pyridiniumbromide), TAMRA-X (6-(tetramethylrhodamine-5(6)-carboxamido)hexanoate);the Orange dyes (Em_(max) 586-647 nm) rhodamine derivatives BODIPY576/589, BODIPY 581/591, ROX (carboxyrhodamine), VIC (Applied BiosystemsInc., Foster City, Calif.), NED (Applied Biosystems Inc., Foster City,Calif.) and the Red dyes (E_(max) 647-700 nm) ascarboxynaphthofluorescein.

A quencher as used herein is a moiety that decreases the light emittedby the fluorophore at the wavelength at which signal is measured, or isa fluorescent moiety that serves to shift the wavelength of lightemitted by the fluorophore of the nucleic acid probe. Quenchers suitablein the context of the present invention include (without limitation)DABCYL (4-(4′-dimethylaminophenylazo)benzoic acid), QSY-7(9-[2-[[4-[[(2,5-dioxo-1-pyrrolidinyl)oxy]carbonyl]-1-piperidinyl]sulfonyliphenyl]-3,6-bis(methylphenylamino)),BHQ-1, BHQ-2, BHQ-3 (Biosearch Technologies Inc., 2003, Cat. Nos.BG5-5041T, BG5-5042T, and BG5-5043T) and TAMRA((6-tetramethylrhodamine-5(6)-carboxamido)hexanoate). Additionally, aquencher can be an organic dye, which may or may not be fluorescent,depending on the embodiment of the invention.

In yet another embodiment, the present invention comprises a probewherein the first and second oligonucleic acids comprise additionalnucleobases that are not complementary to the nucleic acid of interestor to the first nucleic acid, respectively, at the 5′ or the 3′ end.

In another embodiment the present invention comprises a probe whereinthe ratio of the second oligonucleic acid comprising the quencher to thefirst oligonucleic acid comprising the fluorophore may be more than 1.1.Additionally, another embodiment comprises a probe in which the ratio ofthe second oligonucleic acid comprising the quencher to the firstoligonucleic acid comprising the fluorophore may be more than 0.1 andless than 0.9.

In another embodiment of the present inventive probe the firstoligonucleic acid comprises two label moieties, one fluorophore and onequencher. The incorporation of a quencher (in addition to thefluorophore) in the first oligonucleic acid reduces backgroundfluorescent emission (or background signal) that would occur when firstoligonucleic acid is bound neither to target, nor to a secondoligonucleic acid comprising a quencher. Another embodiment comprises aprobe in which the molar ratio of the second oligonucleic acid(comprising a quencher) to the first oligonucleic acid (comprising onefluorophore and one quencher) is more than 0.1 and less than 0.9.Additionally, another embodiment comprises a probe in which the molarratio of the second oligonucleic acid to the first oligonucleic acid(with two label moieties) is more than 1.1.

To improve the fluorescent signal from the nucleic acid probe of thepresent invention, more than one fluorophore may be linked to theoligonucleic acid that binds to the target. Probes of the presentinvention comprising more than one fluorophore preferably emitsubstantially more fluorescent signal than equivalent probes comprisingonly a single fluorophore. Unexpectedly, the probes containing at leastthree fluorophores have been found to be tolerant of mismatches (i.e.,less than perfect complementarity) with target molecules. This can beespecially advantageous when the target nucleic acid is highlypolymorphic as is the case with portions of HIV-1 and otherretroviruses. Because the mismatch tolerance of the probes of thepresent invention is independent of the number of fluorophores attachedto the first oligonucleic acid of the probe, and a probe with more thanone fluorophore shows the same high tolerance for targets with 2, 3 or 4mismatches as a probe of similar length with only one fluorophore, theprobes of the present invention are particularly well suited to thedetection and quantitation of viral target sequences.

In another embodiment, the nucleic acid probe of the present inventioncomprises three oligonucleic acids, the first oligonucleic acidcomprises a fluorophore and the second comprises a quencher. The thirdoligonucleic acid preferably also comprises a quencher. While notdesiring to be bound by any particular theory, it is believed that theincorporation of an additional quencher in the third oligonucleic acidreduces background fluorescent emission (or background signal).Generally, background signal is the emission of fluorescence that is notcaused by binding of a fluorescently labeled oligonucleic acid of theprobe to a target nucleic acid of interest.

In another embodiment, the longer oligonucleic acid comprises a quencherand the shorter oligonucleic acid comprises a fluorophore. Additionally,this embodiment comprises a probe in which the first and the secondoligonucleotides further comprise additional nucleobases that are notcomplementary to the nucleic acid of interest and the firstoligonucleotide, respectively, at the 5′ and 3′ ends. Additionally, boththe first and second oligonucleic acids can also comprise a plurality oflabel moieties. For example, both the first oligonucleic acid and thesecond oligonucleic acid can comprise both a fluorophore and a quencher.Typically, the fluorophore and the quencher are incorporated into theoligonucleic acids such that when bound to an unlabeled oligonucleotidesequence (e.g., a target) the fluorophore and the quencher are separatedand the fluorophore can emit light. However, when the first oligonucleicacid and the second oligonucleic acid of the probe are bound togetherthe fluorophore of the first oligonucleic acid is brought into proximitywith the quencher of the second oligonucleic acid, as well as theconverse (i.e., the fluorophore of the second oligonucleic acid isbrought into proximity with the quencher of the first oligonucleicacid). In this way, both the first and second oligonucleic acids canemit light in the presence of a target, but are mutually quenched in theabsence of the target. Furthermore, the first and second oligonucleicacids of this embodiment may comprise additional nucleobases that arenot complimentary to the nucleic acid of interest or to the firstnucleic acid, respectively, at the 5′ or the 3′ end.

Additionally, this embodiment comprises a nucleic acid probe wherein theratio of the first oligonucleic acid comprising the quencher to thesecond oligonucleic acid comprising the fluorophore is more than 1.1. Inyet another embodiment, the first oligonucleic acid comprises anadditional quencher. This embodiment allows for a probe in which theratio of the first oligonucleic acid to the second oligonucleic acid isMore than 0.1 and less than 0.9. Also, this embodiment allows for aprobe in which the ratio of the first oligonucleic acid to the secondoligonucleic acid is more than 1.1.

In a preferred embodiment, the difference in the fluorescence signalbetween the double stranded form when the fluorophore and quencher areclose, and the target-hybridized state when the fluorophore is separatedfrom the quencher can differ by as much as a factor of 20. This effectis due to the fact that when both are in close proximity there isrelatively efficient quenching of the fluorophore, whereas, when thefirst oligonucleic acid is annealed to the target nucleic acid, it isseparated from the second oligonucleic acid (comprising a quencher) andthe fluorophore is not quenched anymore. As used herein, the terms“quenching” refers to any process whereby when a fluorophore moleculeand a quencher molecule are in close proximity, a substantial loss offluorescence occurs. Including in the group of quenchers arenon-fluorescent molecules and fluorescent molecules, which can acceptlight energy from the fluorophore.

In a preferred embodiment, the 3′ terminal of the first oligonucleicacid only, or together with the 3′ terminal of the second oligonucleicacid of the probe is/are rendered incapable of extension by a nucleicacid polymerase, to prevent interference with the PCR polymerizationstep thereby to prevent reduction of the stepwise efficiency of theamplification.

In another embodiment of the present invention, the first oligonucleicacid, or the first and second oligonucleic acids of the double strandedprobe are rendered impervious to degradation by the 5′→3′ exonucleaseactivity of a nucleic acid polymerase. Preferably, the 5′ end of theoligonucleic acid is rendered resistant to digestion by including one ormore modified internucleotide linkages into the 5′ end of theoligonucleic acid. Minimally, the 5′-terminal internucleotide linkagemust be modified, however, up to all the internucleotide linkages in theoligonucleotide may be modified. Such internucleotide modifications mayinclude modified linkages of the type used in the synthesis ofanti-sense oligonucleotides. Examples of such nuclease resistantlinkages include peptide nucleic acid (PNA) linkages, e.g., Nielsen etal., Science, Vol. 254, pages 1497-1500 (1991), and other likeexonuclease resistant linkages. Alternatively, the 5′ end can berendered resistant to degradation by the 5′-6′ exonuclease activity byadding a sequence that is not complementary to the nucleic acid ofinterest, or by the addition of a derivative moiety at the 5′ end of theoligonucleic acid.

Advantageously, any of the probes described above, each of whichcomprise two oligonucleic acids, can be used in a method of determiningthe presence or quantity of a target nucleic acid. In the followingmethods, any suitable nucleic acid of interest can be the target nucleicacid. The target nucleic acid, however, is preferably RNA, such as aviral RNA or an mRNA. In some embodiments, the target RNA is preferablyreverse transcribed prior to amplification, which amplification is alsopreferably carried out in the same tube and reaction mixture as thereverse transcription step.

The present inventive method of detecting, or quantifying, a nucleicacid of interest in a test sample comprises mixing test sample with DNAamplification reagents to amplify a portion of the nucleic acid ofinterest. The reagents can optionally include reverse transcriptionreagents. The mixture of the amplification reagents and nucleic acid ofinterest is then incubated under suitable conditions to reversetranscribe the target RNA into a target complementary DNA if applicable,and then to amplify the target DNA. The method also comprises adding anucleic acid fluorescent probe comprising a first oligonucleic acid witha fluorophore and a second oligonucleic acid with a quencher such asthose described above, and measuring fluorescence from the fluorescentprobe as an indication of whether the test sample contains the nucleicacid of interest. In some embodiments, the probe is contacted to thenucleic acid of interest before or substantially simultaneously with theamplification reagents, and optionally is mixed with the amplificationreagents prior to contacting the amplification reagents to the nucleicacid of interest. In other embodiments, the probe is contacted to thenucleic acid of interest after incubating the nucleic acid of interestand the amplification reagents under suitable amplification conditions(so as to amplify a portion of the nucleic acid of interest).

Amplification reagents refer to the chemicals, apart from the targetnucleic acid sequence, needed to perform the PCR process. Thesechemicals can conveniently be classified into four classes ofcomponents: (i) an aqueous buffer, often including without limitation amagnesium salt, (ii) amplification substrates, such as fourribonucleotide triphosphates (NTPs) or preferably at least fourdeoxyribonucleotide triphosphates (dNTPs) in polymerization-basedamplification or ATP in ligation-based amplification, (iii) one or moreoligonucleotide primers or probes (normally two primers for each targetsequence, the sequences defining the 5′ ends of the two complementarystrands of the double-stranded target sequence when PCR is employed),and (iv) an amplification enzyme such as a polynucleotide polymerase(for example, Tag polymerase for PCR or RNA polymerase for TMA), or aligase. Additional reagents or additives can also be included at thediscretion of the skilled artisan and selection of these reagents iswithin the skill of the ordinary artisan. Of course, when theamplification reagents are used to cause both reverse transcription andamplification, then reverse transcription reagents are also included inthe amplification reagents. Selection of amplification reagents,according to the method of amplification reaction used, is within theskill of the ordinary artisan.

In embodiments employing “homogeneous” amplification and detectionsteps, i.e., when performing combined amplification and probehybridization detection in a single reaction mixture in a single tube,then: (i) any of the two oligonucleic acids of the probe preferably donot block or otherwise interfere or participate in the PCR or otheramplification step; (ii) neither oligonucleic acid of the probe isdegraded by the enzyme (e.g., by exonuclease activity of a polymeraseenzyme); and (iii) the oligonucleic acids of the probe preferably arenot extended or otherwise modified by the enzyme, e.g., thepolymerization activity of the polymerase.

In another embodiment of the present inventive method, an additionalquantity of the second oligonucleic acid (which comprises a quencher) isadded to the vessel prior to closing the vessel and incubating thereaction mixture under amplification conditions so as to obtain a molarratio of the second oligonucleic acid comprising a quencher to the firstoligonucleic acid comprising a fluorophore that is greater than 1,optionally not less than 1.1 or 1.2, and is less than 20, preferably notgreater than 5, more preferably not greater than 2.5, yet morepreferably not greater than 2, and optionally is not greater than 1.5.

In a preferred embodiment of the inventive method, the probe isprevented from interfering with, or participating in, the PCRpolymerization step by linking to the 3′ terminal end of the nucleicacid an organic or inorganic moiety capable of blocking nucleic acidpolymerization known in the art. Advantageously, this polymerizationblocking moiety can be a fluorophore or a quencher molecule and can beattached to one or both of the oligonucleic acids of the probe by alinking moiety, or by making the 3′-terminal nucleotide adideoxynucleotide. Similarly, the oligonucleic acids of the probe can becompletely or partially a PNA such that the oligonucleic acid of theprobe cannot prime enzyme-mediated polymerization. Alternatively, the 3′end of the oligonucleic acid is rendered impervious to the extensionactivity of a polymerase by including one or more modified polymeraseresistant internucleotide linkages into the 3′ end of theoligonucleotide, such as without limitation a phosphonate orphosphothiorate linkage. Similarly, a non-complementary sequence to thenucleic acid of interest can be attached to the 3′ end of one or both ofthe oligonucleic acids of the probe such that the mismatch impedes orprevents enzyme-mediated polymerization.

In another preferred embodiment, oligonucleic acids of the probe of thepresent invention can be made resistant or impervious to exonucleasedigestion. Suitable methods of impeding or preventing exonucleasedigestion include (without limitation) introducing a 5′ extension thatis not complementary to the nucleic acid of interest, adding anon-phosphodiester linkage between two nucleotidyl bases of theoligonucleic acid, and adding an organic or inorganic blocking moietyknown in the art (per se) to the 5′ end of one or both the oligonucleicacids.

Similarly, enzymatic degradation of the oligonucleic acids of the probecan be impeded or prevented by using an amplification enzyme that lackssuch activity. In the case of amplification-based reactions, forexample, a polymerase which lacks a 5′→3′ exonuclease activity can beused. Polymerases lacking a exonuclease activity are known in the artand include without limitation the Klenow fragment of DNA polymerase I,T4 DNA polymerase, and T7 DNA polymerase, the Stoffel fragment of Taqpolymerase, and other like 5′→3′ exonuclease minus DNA polymerases.

The polymerase optionally can also be rendered inactive, at least withrespect to its exonuclease activity, during the hybridization step. Suchinactivation can be achieved in a number of ways including (i)introducing a temperature sensitive inhibitor into the reaction whichwill inhibit the 5′→3′ exonuclease activity of the polymerase at thehybridization temperature, e.g., a solid adsorbent, a specific antibodymolecule, or other like reversible or irreversible polymeraseinhibitors; (ii) using a polymerase whose activity is greatly reduced atthe hybridization temperature; or (iii) introducing an enzymedeactivation step prior to the hybridization step which irreversiblydeactivates the polymerase enzyme, i.e., an extended period at hightemperature.

In certain embodiments, the reverse transcription efficiency isincreased by using a probe comprising an oligonucleic acid that iscomplementary to a target RNA of interest that has a T_(m) (meltingtemperature) of the first oligonucleic acid to the second oligonucleicacid that is lower than the temperature at which the reaction mixture isincubated during reverse transcription. While not desiring to be boundby any particular theory, it is believed that, by carrying out thereverse transcription step at a temperature above each of the Tm of theprobe, the probe does not compete with the target RNA by competitivelybinding to the enzyme mediating reverse transcription.

Similarly, in embodiments employing reverse transcription in thepresence of the probe, neither (or none) of the oligonucleic acids ofthe probe bind to the target RNA at the temperature at which reversetranscription occurs.

EXAMPLES

The present invention will be further clarified by the followingexamples, which are only intended to illustrate the present inventionand are not intended to limit the scope of the present invention.

Example 1 Effect of the Length Difference Between the Two OligonucleicAcids of a Nucleic Acid Probe on Mismatch Tolerance Evaluated by MeltingCurve Assays

Melting reactions were performed in a Stratagene Mx4000 multiplexquantitative PCR system with the following cycle conditions: 1 cycle ofdenaturation at 95° C. for 3 min; 75 cycles of 1-minute holding at arange of temperatures from 85° C. to 10° C. with an 1° C. decrement percycle. Fluorescein (FAM) fluorescence measurements were recorded duringeach 1-minute hold of the 75 cycles. At the end of each run, the datawere analyzed and melting curves were generated.

Table 2 sets forth the sequences of PCR primers and linear probes usedin this and the following examples.

TABLE 2 Name Sequence PCR Primers FP-295′-ATTCCCTACAATCCCCAAAGTCAAGGAGT-3′ (SEQ ID NO: 1) RP-255′-CCCCTGCACTGTACCCCCCAATCCC-3′(SEQ ID NO: 2) RP-245′-CCCCTGCACTGTACCCCCCAATCC-3′(SEQ ID NO: 3)Linear Probes¹ labeled with FAM 520-206-FAM-(5′)-ACAGCAGTACAAATGGCAGT-(3′)-DABCYL (SEQ ID NO: 4) 520-316-FAM-(5′)-ACAGCAGTACAAATGGCAGTATTCATCCACA-(3′)- DABCYL (SEQ ID NO: 5)lin-41 6-FAM-(5′)- GCTACAGCAGTACAAATGGCAGTATTCATCCACAATTTCCC-(3′)-DABCYL (SEQ ID NO: 6) slin-47 6-FAM-(5′)-GCACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAA-(3′)-DABCYL (SEQ ID NO: 7) dfam-50 6-FAM-(5′)-GCACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAACGC-(3′)-6-FAM (SEQ ID NO: 8) fam-6506-FAM-(5′)-GCACAGCAGTACAAATGGCAGTATTCATCCACAAT(dT-FAM)TTAAAAGAAAACGC-(3′)-6-FAM (SEQ ID NO: 9)Quenching Oligos² labeled with DABCYL que-12(5′)-GTATTGTACTGCTGT-(3′)-DABCYL (SEQ ID NO: 10) que-14(5′)-CGGATTTGTACTGCTGT-(3′)-DABCYL (SEQ ID NO: 11) que-16(5′)-GACCCATTTGTACTGCTGT-(3′)-DABCYL (SEQ ID NO: 12) que-22DABCYL-(5′)-GACCCATTTGTACTGCTGTAGC-(3′)-DABCYL (SEQ ID NO: 13) que-23DABCYL-(5′)-TGAGCCATTTGTACTGCTGTAGC-(3′)-DABCYL (SEQ ID NO: 14)sque-15BH  5′-TTTGTACTGCTGTGC-(3′)-BHQ-1 (SEQ ID NO: 15) bhq-5015BHQ-1-(5′)-GCGTTTTCTTTTAAA-(3′)-BHQ-1 (SEQ ID NO: 16) ¹Sequencessubstantially complementary with targets are underlined (“m”).²Sequences substantially complementary with linear FAM probes areunderlined (“n”).

In each assay, 100 μl reaction contained 1.25×RT-PCR buffer (62.5 mMBicine, pH 8.05-8.25, 143.75 mM potassium acetate, 10% glycerol, 0.125mM EDTA, 0.0125 mg/ml acetylated bovine serum albumin (acetylated-BSA),0.078% (v/v) Tween 20, and 0.025% (w/v) sodium azide), 2.5 mM MnCl₂, 0.2μM FAM-labeled oligonucleic acid (“oligo”), 0.2 μM DABCYL-labeledquenching oligo and 1 μM single-stranded complementary target oligo thatwas 48 nucleotides long and comprised 0, 1, 2, 3, or 4 mismatches withthe FAM labeled oligo (oligos were obtained from Sigma-Genosys). Thelength of the FAM-labeled oligo was either 20 or 31 nucleotides long,while the DABCYL-labeled quenching oligo was 12, 14 or 16 nucleotides inlength. FIGS. 1A-F show the melting curves of a series ofdouble-stranded linear probe sets in the presence or absence of targetoligos with different numbers of mismatches, ranging from 0 to 4. TheFAM fluorescence intensity was measured as,a function of temperature.(A) 520-20/que-16; (B) 520-20/que-14; (C) 520-20/que-12; (D)520-31/que-14; (E) 520-20/que-12; (F) 520-31/que-14. Positions ofmismatches (“mis” hereinafter) for (A)-(C) are as follows: 1 mis is the12^(th) nucleotide; 2 mis are the 12^(th) and 18^(th) nucleotides.Positions of mismatches for (D) are: 1 mis is the 12^(th) nucleotide; 3mis are the 12^(th), 18^(th) and 27^(th) nucleotides. Positions ofmismatches for (E) are; 1 mis is the 3^(rd), 9^(th) or 12^(th); 2 misare the 9^(th) and 12^(th) nucleotides. Positions of mismatches for (F)are following: 1 mis is the 12^(th); 2 mis are the 9^(th) and 27^(th),the 21^(st) and 27^(th), the 24^(th) and 27^(th), the 3^(rd) and 27^(th)or the 9^(th) and 12^(th) nucleotides; 3 mis are the 24^(th), 25^(th)and 27^(th) or the 12^(th), 21^(st) and 27^(th) nucleotides; 4 mis arethe 21^(st), 24^(th), 25^(th) and 27^(th) nucleotides. All mismatchednucleotide positions start from the 5′ end of each respective HIV FAMlinear probe.

At high temperatures, the FAM-labeled oligo and the shortercomplementary DABCYL-labeled quenching oligo of each double-strandedlinear probe set were separated, thus leading to the restoration of FAMfluorescence. In the absence of target oligo, these two oligos tended togradually hybridize with each other as the incubation temperaturedecreased and formed a non-fluorescent duplex due to the close proximityof the fluorophore FAM and the quencher DABCYL. The Tm's of thequenching oligos determined the incubation temperatures at which thenon-fluorescent duplexes started to form. The quenching oligo que-16carrying a length of 16 complementary nucleotides (Table 2) began theformation of the non-fluorescent duplexes at about 60° C. (FIG. 1A),whereas the 14-base (que-14; Table 2) and 12-base (que-12; Table 2)quenching oligos started it at around 55° C. and 50° C., respectively(FIGS. 1B and C). In the presence of target oligos with 0 mismatches,the quenching oligos, which were shorter and thus had lower Tm than thetarget oligos, were unable to compete with the target oligos for bindingto the FAM-labeled oligos, thus resulting in the formation ofprobe-target hybrids that fluoresced (FIGS. 1A-F). In the presence oftarget oligos with mismatches, the 12-base quenching oligo que-12 wasstill unable to compete with the target oligos with 1 or 2 mismatchesfor binding to the 20-base FAM-labeled oligo 520-20 (Table 2) (FIG. 1C);the 14-base quenching oligo que-14, on the other hand, was still unableto compete with the target oligo with 1 mismatch but managed to bind tothe FAM oligo 520-20 in the presence of the target oligo with 2mismatches (FIG. 1B). In contrast, the 16-base quenching oligo que-16was able to bind to 520-20 in the presence of 1 mismatch and even moreso in the presence of 2 mismatches (FIG. 1A). These results demonstratethat extending the length of a quenching oligo reduced the capability ofits complementary FAM-labeled oligo to bind to target oligos withmismatches. In other words, increasing the length difference between theFAM-labeled oligo and its complementary DABCYL-labeled quenching oligoenhances the level of tolerance of the FAM-labeled oligo to targetoligos with mismatches. The same conclusion can be drawn when comparingthe melting curves of linear probe set 520-20/que-14 (FIG. 1B) withthose of 520-31/que-14 (FIG. 1D). The probe set 520-31/que-14 was evenable to pick up the target oligo with 4 mismatches as efficiently as theone with 0 mismatches over a broad range of hybridization. temperatures(FIG. 1F).

Example 2 Effect of the Length Difference Between the Two OligonucleicAcids of a Nucleic Acid Probe on Mismatch Tolerance Evaluated byQuantitative Real-Time RT-PCR Assays

This example shows the evaluations on three different probe sets520-20/que-16, 520-20/que-12 and 520-31/que-14 for their mismatchtolerances by performing the quantitative real-time RT (reversetranscription)-PCR assays. Five transcripts carrying different mutationswere employed to test these three probe sets. In these non-competitivequantitative assays, each 100 pl RT-PCR reaction contained 1.25×RT-PCRbuffer (62.5 mM Bicine, pH 8.05-8.25, 143.75 mM potassium acetate, 10%glycerol, 0.125 mM EDTA, 0.0125 mg/ml acetyl bovine serum albumin (BSA),0.078% (v/v) Tween 20, and 0.025% (w/v) sodium azide), 2.5 mM MnCl₂,0.375 mM of each deoxynucleotide-triphosphate (dATP, dCTP, dGTP, dTTP),13.13 units of rTth DNA polymerase (Applied Biosystems), 0.6 μM HIVforward PCR primer FP-29, 1.6 μM HIV reverse PCR primer RP-25 (Table 2),0.1 μM internal control (IC) forward primer-196, 0.3 μM IC reverseprimer-310, 0.2 μM FAM-labeled oligo probe for detection of the HIV PCRproducts, 0.2 μM DABCYL-labeled quenching oligo for quenchingfluorescence signal of the FAM probe, 0.1 μM VIC-labeled beacon probefor detecting the IC PCR products (all fluorophore-labeled andquencher-labeled oligos obtained from TriLink), 1× FRETROX (AppliedBiosystems) as the reference dye for signal normalization, 5,000 copiesof IC transcript and different levels of HIV wild type transcriptstandards (0, 4.17×10¹, 4.17×10², 4.17×10³, 4.17×10⁴ or 4.17×10⁵ copiesper reaction). To quantify the five transcripts by each of the threeprobe sets, each transcript at 1×10⁴ copies/reaction was used to run theassay along with the wild type transcript standards. Amplificationreactions were performed in an Applied Biosystems 7000 SequenceDetection PCR system with the following cycle conditions: 1 cycle ofreverse transcription at 59° C. 30 min; 2 cycles of low-stringentamplification at 95° C. 1 Min and 54° C. 1 min; 10 cycles ofhigh-stringent amplification at 95° C. 15 sec and 59° C. 1 min; and 40amplification and detection cycles of 95° C. 15 sec and 45° C. 2 min 30sec. Fluorescence measurements were recorded during each 45° C. step ofthe 40 cycles. At the end of each real-time PCR run, the data wasautomatically analyzed by the system and amplification plots wereobtained. Quantities of the five sample transcripts were determined byusing the calibration curve obtained from plotting the log₁₀ HIVstandard copy numbers against their respective fluorescence thresholdcycles (C_(T)). FIGS. 2A-C show the amplification plots of the fivetranscripts by using the three double-stranded linear probe sets520-20/que-16, 520-20/que-12 and 520-31/que-14, respectively. 1×10⁴copies of each transcript were amplified, and the amount of PCR productsgenerated at each cycle was detected by one of the three double-strandedlinear probe sets: (A) 520-20/que-16; (B) 520-20/que-12; (C)520-31/que-14. To the five transcripts, the FAM-labeled oligo 520-20encountered 0 mismatches to two of them and 2 mismatches to theremaining three (Table 4). When paired with the DABCYL-labeled quenchingoligo que-16, the probe 520-20 barely detected the three transcriptswith 2 mismatches (FIG. 2A) and thus under-estimated theirconcentrations by more than 1 log 10 (Table 3). On the other hand, whenpaired with a 4-base shorter quenching oligo que-12, the probe S20-20was able to detect the three 2-mismatch transcripts at a higherefficiency (FIG. 2B) and only under-estimated their quantities by lessthan 0.5 log 10 (Table 4). These results confirmed the conclusion fromExample 1 that widening the length difference between the two componentoligos (the FAM-labeled oligo and its complementary DABCYL-labelingquenching oligo) of a double-stranded linear probe increases theefficiency of the FAM-labeled oligo to pick up target oligos withmismatches. This conclusion was further substantiated by the ability ofthe probe set 520-31/que-14, with a larger length difference of 17 basesbetween the two component oligos, to detect transcripts with mutationsup to 4 almost as efficiently as the wild type transcript (FIG. 2C). Theprobe 520-31, which was 11 bases longer than 520-20 and had to identifymore mismatches for the same set of the five transcripts (Table 5),quantified all five transcripts to be between 1.3×10⁴ and 3.1×10⁴ (Table5); these determined copy numbers were very close to the expected 1×10⁴.In the logo scale, the highest determined copy number difference betweenthe mutant and the wild type was 0.4 log₁₀ that fell within theacceptable 0.5 log₁₀ (Table 5). In conclusion, partially double-strandedprobes can be utilized to accurately quantify nucleic acid samples, andwhen designed appropriately, those probes are able to quantify mutantsas accurately as wild types.

TABLE 3 Quantifications of transcripts (4.0 log10 per reaction) with 0or 2 mismatches by using the double-stranded probe 520-20/que-16 Numberof Positions of Quantity Mismatches Mismatches¹ (log 10 cps/reaction) 0n/a 4.42 0 n/a 4.41 2 6, 12 3.03 2 9, 12 2.90 2 12, 18  3.37 ¹Positionsof mismatches show the positions of mismatched nucleotides starting fromthe 5′ end of the HIV FAM probe 520-20. n/a: not applicable.

TABLE 4 Quantifications of transcripts (4.0 log10 per reaction) with 0or 2 mismatches by using the double-stranded probe 520-20/que-12 Numberof Positions of Quantity Mismatches Mismatches¹ (log 10 cps/reaction) 0n/a 4.47 0 n/a 4.46 2 6, 12 4.03 2 9, 12 4.13 2 12, 18  4.13 ¹Positionsof mismatches show the positions of mismatched nucleotides starting fromthe 5′ end of the HIV FAM probe 520-20. n/a: not applicable.

TABLE 5 Quantifications of transcripts (4.0 log10 per reaction) with 0,2, 3 or 4 mismatches by using the double-stranded probe 520-31/que-14Number of Positions of Quantity Mismatches Mismatches¹ (log 10cps/reaction) 0 n/a 4.50 2 6, 12 4.31 3 9, 12, 22 4.31 3 12, 18, 27 4.114 21, 24, 25, 27 4.31 ¹Positions of mismatches show the positions ofmismatched nucleotides starting from the 5′ end of the HIV FAM probe520-31. n/a: not applicable.

Example 3 Inhibition of RT-PCR by a Quenching Oligonucleotide with a TmHigher than the RT Temperature

To examine the impact of utilizing a quencher probe with a Tm that isabove the incubation temperature of the RT reaction, performance of theprobe combination, lin-41 and que-23 (Table 2), was evaluated in aquantitative real-time reverse transcription (RT)-PCR assay. Thequenching oligo, que-23, has a Tm of 60.27, above the 59° C. RTincubation temperature. In this competitive quantitative assay, each 100μl RT-PCR reaction was carried out in the presence of 1×EZ buffer(containing 50 mM Bicine, pH 8.2, 115 mM potassium acetate and 8%glycerol), 2.5 mM Mn(OAc)2, 0.4 mM of each deoxynucleotide-triphosphate(dATP, dCTP, dGTP, dTTP), 20 units of RNase inhibitor, 10 units of TthDNA polymerase (all from Applied Biosystems), 0.2 μM HIV forward PCRprimer FP-29, 1.0 μM HIV reverse PCR primer RP-24, 0.1 μM FAM-labeledoligo probe lin-41 for detection of the HIV wild type PCR products, 0.2μM DABCYL-labeled quenching oligo que-23 to quench the FAM probe, 0.1 μMTexas Red-labeled beacon probe bpic-7 for detecting the internal control(IC) PCR products, 0.04 μg/ml Alexa (Molecular Probes) as the referencedye for signal normalization, 100 copies of internal control transcriptand different copy numbers of HIV wild type transcript (0, 10, 10², 10³,10⁴, 10⁵ or 10⁶ copies). Amplification reactions were performed in aStratagene Mx4000 multiplex quantitative PCR system with the followingcycle conditions: 1 cycle of reverse transcription at 95° C. 5 sec and59° C. 30 min; 2 cycles of low-stringent amplification at 95° C. 30 sec,54° C. 30 sec and 72° C. 30 sec; 10 cycles of high-stringentamplification at 95° C. 30 sec, 59° C. 30 sec and 72° C. 30 sec; 33amplification and detection cycles of 95° C. 30 sec, 50° C. 1 min and72° C. 30 sec. Fluorescence measurements were recorded during each 50°C. step of the 33 cycles. At the end of each real-time PCR run, the datawas automatically analyzed by the system and amplification plots wereobtained. Amplification curves of the wild type and the internal controltranscripts are shown in FIGS. 3A and B, respectively. Seven reactions,each initiated with a different number of HIV wild type templatetranscripts were incubated simultaneously in a Stratagene's Mx4000. Theconcentration of amplicons that were present after each cycle ofamplification was determined by measuring FAM fluorescence signalemanated from the probe-target hybrids during the last 21 seconds of theannealing step. The FAM fluorescence intensity in each reaction wasmeasured as a function of cycle. Of the wild type transcript inputlevels ranging from 10¹-10⁶, significant amplification was observed onlyfor the high copy numbers (i.e. from 10⁴ to 10⁶), whereas nofluorescence signals were recorded for the low copy numbers from 0 to10³. For real-time RT-PCR amplification of control transcripts, 100copies of internal control transcripts were used. The amount of internalcontrol PCR products generated at each cycle was detected by molecularbeacon probe bpic-7 labeled with Texas Red. The copy number of wild typetranscript as indicated next to each curve was amplified in an RT-PCRreaction together with the 100 copies of internal control transcript. Nofluorescence signals were observed for the 100 copies of internalcontrol transcript. These data are consistent with a hypothesis thatthe-DABCYL-labeled quenching oligo que-23 with a Tm of 60.27, higherthan the 59° C. RT temperature, hybridized to the FAM-labeled linearprobe lin-41 and that the lin-41/que-23 duplex inhibited reversetranscription. The inhibition significantly reduced reversetranscription efficiency of both wild type and internal controltranscripts. No fluorescence signals above baseline were observed at lowcopy numbers (0-10³), while amplification curves for the high copynumbers (10⁴-10⁶) had significantly delayed cycle numbers and reachedsub-maximal levels.

Example 4 Elimination of Inhibition by a Quenching Oligonucleic Acidwith a Tm Lower than the RT Temperature in RT-PCR

To evaluate the relationship between the Tm of the quenching oligo andRT-PCR assay performance, the FAM-labeled probe, lin-41, was used incombination with the quenching oligo, que-22 (Table 2). The oligo,que-22, has a Tm of 55.86° C., below the 59° C. incubation temperatureof reverse transcription (RT). A quantitative real-time RT-PCR assay wasperformed as described in Example 3, with the exception that thequenching oligo, que-22, was substituted for que-23. The resulting datais presented in FIGS. 4A and 4B. In contrast to results obtained inExample 3, typical amplification curves were found for both wild typeand internal control transcripts at all copy levels. The wild typeamplification curves at template concentrations of 10⁴, 10⁵ and 10⁶emerged about 8 cycles earlier and reached to a maximum level higherthan 10,000. Even at 10 copies per reaction, the lowest template inputlevel examined, significant amplification was observed 2,000 units). Theobserved amplification was significantly above the baseline,demonstrating that the probe combination, lin-41/que-22, provides highsensitivity. Moreover,the assay exhibited good linearity with a broaddynamic range; correlation coefficient (r²) of 0.998 over six logs (10to 10⁶) of target concentration. For the 100 copies of internal controltranscript, the amplification curves displayed a typical profile ofcompetitive PCR, in which the internal control fluorescence signalsdecreased in response to the increase of wild type transcript copynumbers. These data demonstrate the utility of a quenching probe thathas a Tm (for the FAM-labeled linear probe) below the RT incubation stepfor RT-PCR amplification and quantification.

Example 5 Signal Enhancements by Using Linear Probes Labeled with Morethan One Fluorescent Molecule

To examine whether fluorescence signals generated in RT-PCR assays couldbe enhanced by use of linear probes carrying more than one fluorescentlabel, a quantitative real-time RT-PCR. assay was set-up with multiplylabeled probes. Three FAM-labeled linear probes, slin-47, dfam-50 andfam-650 (Table 2) were used, along with two quenching oligos, sque-15BHand bhq-5015. Both quenching oligo probes bind to all three FAM-labeledlinear probes. Probe slin-47 carries one FAM (1×FAM) at the 5′ end and aDABCYL at the 3′ end, while probe dfam-50 has one FAM at both 5′ and 3′ends (2×FAM); probe fam-650 possesses an internal FAM in addition to itstwo terminal FAMs (3×FAM). The RT-PCR reactions in this competitivequantitative assay were carried out under the condition similar to thatdescribed in Example 3. Each 100 μl RT-PCR reaction contained 1×EZbuffer (containing 50 mM Bicine, pH 8.2, 115 mM potassium acetate and 8%glycerol), 2.5 mM Mn(OAc)2, 0.4 mM of each deoxynucleotide-triphosphate(dATP, dCTP, dGTP, d′ITP), 20 units of RNase inhibitor, 10 units of TthDNA polymerase,(all from Applied Biosystems), 0.1 μM HIV forward PCRprimer FP-29, 1.0 μM HIV reverse PCR primer RP-24, 0.2 μM FAM-labeledoligo probe (slin-47, dfam-50 or fam-650) for detection of the HIV wildtype PCR products, 0.25 μM BHQ-labeled quenching oligo sque-15BH toquench the 5′ end of the FAM probe, 0.25 μM BHQ-labeled quenching oligobhq-5015 to quench the 3′ end of the FAM probe, 0.2 μM Texas Red-labeledbeacon probe bpic-7BH for detecting the internal control (IC) PCRproducts, 0.04 μg/ml Alexa as the reference dye for signalnormalization, 100 copies of internal control transcript and differentcopy numbers of HIV wild type transcript (0, 10, 10², 10³, 10⁴, 10⁵ or10⁶ copies). Amplification reactions were performed in a StratageneMx4000 multiplex quantitative PCR. system with the following cycleconditions: 1 cycle of reverse transcription at 59° C. 60 min; 2 cyclesof low-stringent amplification at 95° C. 1 min and 54° C. 1 min; 10cycles of high-stringent amplification at 95° C. 15 sec and 59° C. 1min; 33 amplification and detection cycles of 95° C. 15 sec and 40° C. 2min 30 sec. Fluorescence measurements were recorded during each 40° C.step of the 33 cycles. At the end of each real-time PCR run, the datawere automatically analyzed by the system and amplification plots wereobtained. Typical amplification profiles were observed at all inputlevels of wild type transcript by all three FAM-labeled probes. FIG. 5depicts amplification plots for wild type transcript at 10copies/reaction (A), 10³ copies/reaction (B), 10⁵ copies/reaction (C)and 10⁶ copies/reaction (D). At each copy number tested, the 3×FAM probeoverall generated more fluorescence signal than the 2×FAM probe, whichin turn overall emanated more signal than the 1×FAM probe. In additionto an overall higher fluorescence signal level, increasing assaysensitivity, linear probes with multiple FAM labels generatedamplification curves with steeper slopes, facilitating determination ofthe fluorescence threshold cycle (C_(T)).

Example 6 Quantification of Transcripts with or Without Mutations

To examine the utility of partially double-stranded probes for reliablydetecting and quantifying templates with mismatches, probe set fam-650(3 FAM labels)/sque-15BH+bhq-5015 (Table 2) was used to quantifytranscripts with multiple mutations. Each of five transcripts carrying0, 2, 3, 4 or 5 mutations was quantified in a real-time RT-PCR assay.Transcript copy number was determined by OD260 measurement. The assaywas standardized using different copy numbers of wild type transcript.The RT-PCR reactions in this competitive quantitative assay were carriedout under the condition similar to that described in Example 5. Each 100μl RT-PCR reaction contained 1×EZ buffer (containing 50 mM Bicine, pH8.2, 115 mM potassium acetate and 8% glycerol), 2.5 mM Mn(OAc)2, 0.4 mMof each deoxynucleotide-triphosphate (dATP, dCTP, dGTP, dTTP), 20 unitsof RNase inhibitor, 10 units of Tth DNA polymerase, 0.1 μM HIV forwardPCR primer FP-29, 1.0 μM HIV reverse PCR primer RP-24, 0.15 μMFAM-labeled oligo probe fam-650 for detection of the HIV wild type PCRproducts, 0.25 _(I)tM BHQ-labeled quenching oligo sque-15BH to quenchthe 5′ end of the FAM probe, 0.25 μM BHQ-labeled quenching oligobhq-5015 to quench the 3′ end of the FAM probe, 0.1 μM Texas Red-labeledlinear probe trp-34 for detecting the internal control (IC) PCRproducts, 0.1 μM BHQ-labeled quenching oligo etrp-15bhq to quench theTexas Red IC, 0.04 μg/ml Alexa as the reference dye for signalnormalization, 200 copies of internal control transcript and differentcopy numbers of HIV wild type standard transcript (0, 10, 10², 10³, 10⁴,10⁵ or 10⁶ copies). To quantify the five transcripts, 8×10³ copies ofeach transcript instead of the wild type standard were added into oneRT-PCR reaction and amplified along with the seven HIV standards.Amplification reactions were performed in a Stratagene Mx4000 multiplexquantitative PCR system with the following cycle conditioris; 1 cycle ofreverse transcription at 59° C. 60 min; 2 cycles of low-stringentamplification at 95° C. 1 min and 54° C. 1 min; 10 cycles ofhigh-stringent amplification at 95° C. 15 sec and 59° C. 1 min; 33amplification and detection cycles of 95° C. 15 sec and 40° C. 2 min 30sec. Fluorescence measurements were recorded during each 40° C. step ofthe 33 cycles. At the end of each real-time PCR run, the data wereautomatically analyzed by the system and amplification plots wereobtained. FIG. 6 shows the amplification plots of the five transcripts.All five curves group together and emerge up at cycle 15. The copynumbers of the five transcripts determined by this quantitative assayturned out to be 9.6×10³ (0 mismatches), 1.1×10⁴ (2 mismatches), 7.2×10³(3 mismatches), 5.6×10³ (4 mismatches) and 6.3×10³ (5 mismatches); thesecopy numbers were very close to the expected 8×10³. In the log₁₀ scale,the highest difference among these five determined copy numbers was 0.29log₁₀. Thus, the partially double-stranded linear probe set quantifiedtranscripts with up to five mutations as accurately as the wild type (0mismatches). This demonstrates the tolerance of partiallydouble-stranded probes to mismatches and demonstrates their utility forquantifying target regions containing genetic polymorphisms.

1. A composition comprising a pair of labeled nucleotide sequences, thefirst member of the pair being selected from the group consisting of[SEQ ID NO: 4], [SEQ ID NO: 5], [SEQ ID NO: 6], [SEQ ID NO: 7], [SEQ IDNO: 8] and [SEQ ID NO: 9] and; the second member of the pair beingselected from the group consisting of [SEQ ID NO: 10], [SEQ ID NO: 11],[SEQ ID NO: 12], [SEQ ID NO: 13], [SEQ ID NO: 14], [SEQ ID NO: 15] and[SEQ ID NO: 16].
 2. The composition of claim 1, wherein the first memberof the pair is labeled with a fluorescent label and the second member ofthe pair is labeled with a quencher.
 3. The composition of claim 1,wherein the first member of the pair is labeled with a quencher and thesecond member of the pair is labeled with a fluorescent label.
 4. Thecomposition of claim 1, wherein said pairs of labeled nucleotidesequences are selected from the group consisting of [SEQ ID NO: 4] and[SEQ ID NO: 10]; [SEQ ID NO: 4] and [SEQ ID NO: 11]; [SEQ ID NO: 4] and[SEQ ID NO: 12]; [SEQ ID NO: 5] and [SEQ ID NO: 10]; [SEQ ID NO: 5] and[SEQ ID NO: 11]; [SEQ ID NO: 5] and [SEQ ID NO: 12].
 5. The compositionof claim 4, wherein the one member of the labeled pairs of nucleotidesequences is labeled with a fluorescent label and the other member ofthe labeled pairs of nucleotide sequences is labeled with a quencher. 6.A composition comprising a labeled nucleotide sequence selected from oneor more of [SEQ ID NO: 1], [SEQ ID NO: 2], [SEQ ID NO: 3], [SEQ ID NO:4], [SEQ ID NO: 5], [SEQ ID NO: 6], [SEQ ID NO: 7], [SEQ ID NO: 8], [SEQID NO: 9], [SEQ ID NO: 10], [SEQ ID NO: 11], [SEQ ID NO: 12], [SEQ IDNO: 13], [SEQ ID NO: 14], [SEQ ID NO: 15] and [SEQ ID NO: 16].
 7. Thecomposition of claim 6, wherein said label on said nucleotide sequenceis a fluorescent label.
 8. The composition of claim 6, wherein saidlabel on said nucleotide sequence is a quencher.